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Both endangered and non‐endangered unionid mussels are heterogeneously distributed within the Allegheny River, Pennsylvania. Mussel populations vary from high to low density downstream of Kinzua Dam, and the direction, amount, and range of hyporheic exchange (seepage) at the sediment–water interface were suspected to influence their distribution and abundance. Nineteen hydrogeomorphic variables, including the quantification of seepage metrics, substrate size, river stage, river discharge, and shear stress, were measured at five reaches on the Allegheny River within 80 km downstream of Kinzua Dam. Analysis revealed significant (α = 0·05) non‐linear correlations between mussel population density and directional mean seepage (positive relationship), river width (positive relationship), and median substrate size (negative relationship). Specifically, seepage findings showed that increases in upward seepage and decreases in the overall range of seepage related to increases in mussel population density. River width, directional mean seepage, and median substrate size were also found to co‐vary with marginal significance (α = 0·1), making their individual influences on mussel population density uncertain. Absolute mean seepage, water depth, hydraulic head, temperature differences between the surface water and substrate, and other substrate metrics besides median grain size were not found to significantly correlate to mussel population density. Considering the physical processes often linking seepage to other explanatory variables, future research in seepage–mussel relationships should work to isolate the mechanistic influence of hyporheic exchange independently from its common covariation with substrate size and geomorphology. Copyright © 2014 John Wiley & Sons, Ltd.

Fecal pollution of water systems can exact high risks to human health and can result in significant economic losses due to closures of beaches and shellfish harvesting areas. The ability to effectively track the sources of pollution within a watershed is imperative for proper risk assessment and remedial efforts to be evaluated and enacted. Several microbiological, genotypic, phenotypic, and chemical methods have been proposed as useful tools for tracking the sources of fecal pollution. Here, we describe the effective use of the ribotyping microbial source tracking procedure to determine the source(s) of Escherichia coli within a South Carolina watershed. In this study, 92% of animal-derived E. coli isolates collected were correctly classified as being of animal origin using our existing ribotype profile database. These results suggest that the temporal and spatial diversity of E. coli may not be a significant factor in broad source (human versus animal) classification of E. coli by using our ribotyping DNA fingerprinting procedure. In addition, direct matching of ribotype profiles from water samples to those from known animal sources was used as an index of the potential predominant sources of fecal input(s) into this watershed. This method was useful in assessing possible specific animal sources when statistical analysis of a ribotype profile indicated general animal fecal pollution. Prior to investigating potential fecal inputs into this watershed, a significant human source was suspected as the primary input; however, of the 515 E. coli isolated from water samples collected during the course of this study, 88% were typed as being of animal fecal origin. Thus, this study was integral in the realization that animals may be a significant source of contamination and that remediation efforts should be redirected to accommodate these findings. This study summarizes one of the few case studies in which ribotyping was successfully utilized to further resolve a "true-life" water quality and management problem.

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